data_8Y2L
#
_model_server_result.job_id            Qv7MjKRcwNv9IrhLQ3uXhg 
_model_server_result.datetime_utc      '2025-02-23 23:14:32' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          8y2l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":602}' 
#
_entry.id    8Y2L 
#
_exptl.entry_id    8Y2L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            8Y2L 
_cell.length_a            155.166 
_cell.length_b            268.755 
_cell.length_c            194.862 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Y2L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 G N N 
? 3 I N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD2 ASP 291 A ASP 288 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? 
metalc ? metalc2 A OE1 GLU 518 A GLU 515 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.743 ? 
metalc ? metalc3 A OG SER 521 A SER 518 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? 
metalc ? metalc4 D MN MN . A MN 601 1_555 E O1A UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? 
metalc ? metalc5 D MN MN . A MN 601 1_555 E O3B UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? 
metalc ? metalc6 B OD2 ASP 291 B ASP 288 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.729 ? 
metalc ? metalc7 B OE1 GLU 518 B GLU 515 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? 
metalc ? metalc8 B OG SER 521 B SER 518 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? 
metalc ? metalc9 F MN MN . B MN 601 1_555 G O1A UDP . B UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.756 ? 
metalc ? metalc10 F MN MN . B MN 601 1_555 G O3B UDP . B UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc11 C OD2 ASP 291 C ASP 288 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? 
metalc ? metalc12 C OE1 GLU 518 C GLU 515 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? 
metalc ? metalc13 C OG SER 521 C SER 518 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? 
metalc ? metalc14 H MN MN . C MN 601 1_555 I O1A UDP . C UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? 
metalc ? metalc15 H MN MN . C MN 601 1_555 I O3B UDP . C UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N1 C2 UDP sing 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     8Y2L 
_atom_sites.fract_transf_matrix[1][1]    0.006445 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003721 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.005132 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
D 2 MN A 1 601 1 MN MN . 
E 3 UDP A 1 602 1 UDP UDP . 
F 2 MN B 1 601 2 MN MN . 
G 3 UDP B 1 602 2 UDP UDP . 
H 2 MN C 1 601 3 MN MN . 
I 3 UDP C 1 602 3 UDP UDP . 
J 4 HOH A 1 701 1 HOH HOH . 
J 4 HOH A 2 702 4 HOH HOH . 
J 4 HOH A 3 703 6 HOH HOH . 
J 4 HOH A 4 704 12 HOH HOH . 
J 4 HOH A 5 705 5 HOH HOH . 
K 4 HOH B 1 701 2 HOH HOH . 
K 4 HOH B 2 702 8 HOH HOH . 
K 4 HOH B 3 703 9 HOH HOH . 
K 4 HOH B 4 704 13 HOH HOH . 
L 4 HOH C 1 701 3 HOH HOH . 
L 4 HOH C 2 702 10 HOH HOH . 
L 4 HOH C 3 703 11 HOH HOH . 
L 4 HOH C 4 704 14 HOH HOH . 
L 4 HOH C 5 705 7 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N1 UDP . . . G 3 37.533 95.707 -15.65 1 168.03 0 N1 UDP 602 B 1 
HETATM 2 C C2 UDP . . . G 3 37.624 97.048 -15.984 1 166.03 0 C2 UDP 602 B 1 
HETATM 3 N N3 UDP . . . G 3 37.979 97.295 -17.287 1 167.18 0 N3 UDP 602 B 1 
HETATM 4 C C4 UDP . . . G 3 38.247 96.361 -18.27 1 167.4 0 C4 UDP 602 B 1 
HETATM 5 C C5 UDP . . . G 3 38.13 94.997 -17.847 1 166.86 0 C5 UDP 602 B 1 
HETATM 6 C C6 UDP . . . G 3 37.784 94.723 -16.579 1 168.25 0 C6 UDP 602 B 1 
HETATM 7 O O2 UDP . . . G 3 37.407 97.951 -15.187 1 166.64 0 O2 UDP 602 B 1 
HETATM 8 O O4 UDP . . . G 3 38.554 96.74 -19.4 1 168.89 0 O4 UDP 602 B 1 
HETATM 9 C C1' UDP . . . G 3 37.154 95.375 -14.258 1 173.3 0 C1' UDP 602 B 1 
HETATM 10 C C2' UDP . . . G 3 35.656 95.095 -14.1 1 176.07 0 C2' UDP 602 B 1 
HETATM 11 O O2' UDP . . . G 3 35.136 95.905 -13.068 1 170.92 0 O2' UDP 602 B 1 
HETATM 12 C C3' UDP . . . G 3 35.603 93.601 -13.746 1 182.18 0 C3' UDP 602 B 1 
HETATM 13 C C4' UDP . . . G 3 36.978 93.35 -13.111 1 185.24 0 C4' UDP 602 B 1 
HETATM 14 O O4' UDP . . . G 3 37.861 94.22 -13.858 1 180.51 0 O4' UDP 602 B 1 
HETATM 15 O O3' UDP . . . G 3 34.554 93.322 -12.827 1 181.1 0 O3' UDP 602 B 1 
HETATM 16 C C5' UDP . . . G 3 37.504 91.934 -13.152 1 190.65 0 C5' UDP 602 B 1 
HETATM 17 O O5' UDP . . . G 3 36.559 91.067 -13.837 1 200.26 0 O5' UDP 602 B 1 
HETATM 18 P PA UDP . . . G 3 37.07 89.685 -14.475 1 209.38 0 PA UDP 602 B 1 
HETATM 19 O O1A UDP . . . G 3 35.969 88.671 -14.43 1 207.49 0 O1A UDP 602 B 1 
HETATM 20 O O2A UDP . . . G 3 37.748 89.964 -15.777 1 197.83 0 O2A UDP 602 B 1 
HETATM 21 O O3A UDP . . . G 3 38.172 89.231 -13.402 1 221.16 0 O3A UDP 602 B 1 
HETATM 22 P PB UDP . . . G 3 38.1 88.068 -12.283 1 234.89 0 PB UDP 602 B 1 
HETATM 23 O O1B UDP . . . G 3 38.188 88.768 -10.95 1 243.9 0 O1B UDP 602 B 1 
HETATM 24 O O2B UDP . . . G 3 39.278 87.16 -12.545 1 228.05 0 O2B UDP 602 B 1 
HETATM 25 O O3B UDP . . . G 3 36.763 87.377 -12.499 1 214.92 0 O3B UDP 602 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#